Grain yield of rice is one of the most important ultimate traits in rice production. It is a composite trait of number of grains per panicle, number of effective ears and weight per thousand grains. The number of grains per panicle is dependent on number of spikelets per panicle and seed setting rate. Extensive research has shown that the number of spikelets per panicle determines rice yield to a great extent due to its relatively higher heritability and bigger contribution to yield and therefore much attention has been paid to this trait. Heading date is an important biological trait that directly determines the ecoadaptation and season adaptation of rice varieties. And plant height is closely related to biological yield and the harvest index and influences the stability of yield. Therefore, elucidation of the genetic basis and molecular mechanism of number of grains per panicle, heading date and plant height may facilitate the modification of high yield and yield stability of rice.
Heading date is under the regulation of basic nutritional genes and photoperiod-sensitivity genes (Tanisaka et al. Jpn J Breeding, 1997, 442: 657-668; Tsai, Rice genet Newslett, 1985, 2:77-78). The regional distribution of rice varieties and differentiation of indica rice and japonica rice are also believed to be associated with the evolution of heading date genes. Therefore, revelation of the genetic basis of heading date may lend clues to research on rice evolution and provide theoretical guidance on the breeding selection of rice varieties of different ecotypes. As demonstrated by both classical genetics means and molecular genetics means, heading date is controlled by several qualitative trait loci and many quantitative trait loci (QTLs). Among the QTLs, a heading date QTL in the C1023-R1440 region near the centromere of the rice chromosome 7 (this QTL was named as Ghd7 in the present invention) was detected in different rice populations such as population of the Indica-Japonica cross (Li et. al., 2003, Theor. Appl. Genet. 108: 141-153), population of the Indica-Indica cross (Xing et. al., 2002, Theor. Appl. Genet. 105:248-257), population of the Japonica-Japonica cross (Lin et. al., 2003, Breeding Sci. 53: 51-59) and wild-cultivated population (Thomson et. al., 2003, Theor. Appl. Genet. 107: 479-493), but its genetic effect differed greatly among different populations. Our laboratory, using Zhenshan 97/Minghui 63 derived F2:3 and recombinant inbred line population, also detected a QTL controlling heading date in the Ghd7 region many times, which explained up to about 25% of total heading date variation (Xing et. al., 2001, Acta. Bot. Sin. 43:721-726; Yu et. al., 2002, Theor. Appl. Genet. 104: 619-625). These results showed that Ghd7 gene can be stably expressed under different genetic backgrounds and in different environments. Genetics research of many years suggest that plant height is also controlled by several qualitative trait loci and many QTLs. A QTL that influences plant height and is affected by the environment was also found present in the Ghd7 region in different populations (Li et. al., 1996, Genetics, 145: 453-465; Li et. al., 2003, Theor. Appl. Genet. 108: 141-153; Li et. al., 2006, The New Phyto. 170: 185-193; Xiao et. al., 1996, Theor Appl Genet, 92: 230-244). Also, a QTL that influences grain yield trait was detected in this region in some populations (Brondani et. al., 2002, Theor Appl Genet, 104: 1192-1203; Li et. al., 1996, Genetics). We cultivated the Zhenshan 97/Minghui 63 F2, RIL and “Yongjiu F2” populations in the same season of different years in the same location, and found that this QTL was capable of controlling heading date, plant height, number of spikelets per panicle and yield in the populations of different generations derived from the same combination (Yu et. al., 1997, Proc. Natl. Acad. Sci. USA 94:9226-9231; Xing et. al., 2001, Acta. Bot. Sin. 43:721-726; Yu et. al., 2002, Theor. Appl. Genet. 104:619-625; Xing et. al., 2002, Theor. Appl. Genet. 105:248-257; Hua et. al., 2002, Genetics 162:1885-1895). This has not been reported by other research groups. Ghd7 influenced number of spikelets per panicle, heading date and plant height at the same time. The Minghui 63 allele increased the phenotype values of these three traits. Therefore, there is great potential and prospect for Ghd7 in the modification of rice yield and variety adaptation. Accurate mapping and cloning of Ghd7 may provide a novel gene resource for the high-yield breeding of rice.
It is almost impossible to accurately map the quantitative trait loci using primary mapping population, because in such a population many QTLs that influence the same trait are isolated. The interference among the QTLs and the influence of environmental factors greatly limit the accuracy of QTL mapping. In addition, for a QTL-rich region, it is very difficult to judge whether it is one pleiotropic QTL or many minor QTLs that play a role (Yano et. al., 1997, Plant Molecular Biology 35:145-153). Therefore, advanced mapping populations must be constructed in order to accurately map QTL. A common practice is construction of near isogenic lines of the target QTL to eliminate most of the background difference outside the target QTL site so that the site exhibits typical Mendelian inheritance, that is, conversion of quantitative traits to qualitative traits. This approach has played an important role in the accurate mapping and gene cloning research of many QTLs. Fan et. al. have mapped GS3 to a 7.9 kb region and conducted map-based cloning of GS3 using this approach (Fan et al., 2006, Theo Appl Genet. 112: 1164-1171). Due to the restriction of population size or the frequently-occurred recombination inhibition in the region near the centromere, sometimes the resolution of gene mapping is insufficient to locate the target gene, and this brings trouble to map-based cloning. So a candidate gene cloning approach is a relatively good strategy. All the genes in the mapping region are analyzed; based on the characteristics and relevant functions of the cloned gene domain and by comparison of the functions of known genes and profiles of predicted genes, structurally and functionally relevant genes are selected as the candidate genes for functional verification. This candidate gene strategy provided a new approach for the separation and cloning of Ghd7 gene.
A gene, Ghd7, that controls grain yield, heading date and plant height in rice was isolated and cloned through candidate gene cloning approach in the present invention, to provide a novel gene resource for breeding rice in terms of yield and variety and to lend clues to research on the evolution of crops.